[BioSQL-l] biosql-ora BS-prepopulate-db errors

[Hilmar Lapp]

I committed the other API to the repository, BS-create-Biosql-API2.sql.

Note that some names are still different because of reserved word 
issues. E.g., comment and synonym are reserved in Oracle, so the 
Comment table is named Anncomment, and Term_Synonym.Synonym becomes 
Term_Synonym.Name.

	-hilmar

On Jul 26, 2004, at 1:54 PM, Michael Griffith wrote:

> Hilmar,
>
> Thank you.
>
> From an outsider's view, this all seems a little broken.  Wouldn't it
> benefit the community to bundle all these things together?
>
> Thanks in advance!
>
> MG
>
>
> On 7/26/04 3:21 PM, "Hilmar Lapp" <hlapp at gnf.org> wrote:
>
>> I see. You didn't say Biojava and Biosql Oracle in the same sentence
>> before did you.
>>
>> Biojava can't deal with different 'versions' of the same schema even 
>> if
>> it's only column names, and the Oracle version differs in naming
>> conventions. There is an adaptor API in the repository that maps table
>> names, but you'll need another one that I've written that maps both
>> tables and column names through views. I'll dig that up and post it.
>>
>> Also, the Biojava folks I believe added a table or a column to one of
>> the ontology tables. You'll have to inquire about that on the biojava
>> mailing list.
>>
>> -hilmar
>>
>>
>>
>> On Jul 26, 2004, at 12:24 PM, Michael Griffith wrote:
>>
>>> Hilmar,
>>>
>>> Thanks for the reply.
>>>
>>> I guess I don't really need it, I was just trying to put some data in
>>> the
>>> DB, so I could play with it.  My bigger problem is that once I built
>>> the DB
>>> and tried to insert a record using BioJava 1.4, I got a message that
>>> the
>>> schema was old and I should have used a new schema.
>>>
>>> I posted that message on BioJava mail list, but have received no
>>> reply.  Is
>>> this a question you can help me with?
>>>
>>> Where can I download the bio-sql-ora scripts that will work with
>>> BioJava
>>> 1.4?
>>>
>>> Thanks in advance!
>>>
>>> MG
>>>
>>>
>>> On 7/26/04 2:10 PM, "Hilmar Lapp" <hlapp at gnf.org> wrote:
>>>
>>>> Sorry, the prepopulate script is old and I believe out of date 
>>>> w.r.t.
>>>> some schema changes. 'Cat_Name' should read 'Ont_Name'. It may work
>>>> after that change.
>>>>
>>>> You will want to carefully review what this script does; it's 
>>>> entirely
>>>> custom and nothing in a plain biosql installation depends on it, nor
>>>> does load_seqdatabase.pl. It populates some early versions of custom
>>>> and small ontologies that make up part of the glue in a Symgene
>>>> database, and may be completely useless for other applications.
>>>>
>>>> Let me know if you really want that content and I'll update the
>>>> script.
>>>> I also have dagflat versions of some of those ontologies.
>>>>
>>>> -hilmar
>>>>
>>>> On Jul 22, 2004, at 8:04 AM, Michael Griffith wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am trying to setup BIOSQL to work with Oracle 9i.  I was able to
>>>>> successfully create the database and all of the objects in it.
>>>>> Everything
>>>>> seems to be ok, but when I try to execute the prepopulate-db 
>>>>> script,
>>>>> I
>>>>> get
>>>>> an exception when the script tries to insert into SLGD_Terms.
>>>>>
>>>>> The sql that causes the exception is:
>>>>>
>>>>> --
>>>>> -- Ontology terms: relationship type ontology
>>>>> --
>>>>> INSERT INTO SGLD_Terms (Trm_Name, Trm_Identifier, Cat_Name)
>>>>> VALUES ('EST','REO:0000345','Relationship Type Ontology');
>>>>>
>>>>> The exception is:
>>>>> ORA-20101: failed to lookup Ont <>
>>>>> ORA-06512: at "BIOSQL_APP.TRM" line 102
>>>>> ORA-06512: at "BIOSQL_APP.BIR_TERMS" line 6
>>>>> ORA-04088: error during execution of trigger "BIOSQL_APP.BIR_TERMS"
>>>>>
>>>>> Where BIOSQL_APP is my user.  I have looked at the procedures and
>>>>> triggers
>>>>> involved, and I see that the exception is being raised from the
>>>>> procedure
>>>>> TRM, because of what I think is a broken relationship.
>>>>>
>>>>> What is confusing to me is that the BS-prepopulate-db.sql script 
>>>>> has
>>>>> a
>>>>> comment that reads:
>>>>>
>>>>> -- The following will be created automatically upon inserting their
>>>>> terms.
>>>>> --    'Relationship Type Ontology'
>>>>> --    'Bioentry Type Ontology'
>>>>> --    'Qualifier Type Ontology'
>>>>> --
>>>>>
>>>>> Evidently, this did not happen.  Am I missing something?  Any help
>>>>> would be
>>>>> greatly appreciated!
>>>>>
>>>>> Cheers!
>>>>>
>>>>> Michael Griffith
>>>>>
>>>>> _______________________________________________
>>>>> BioSQL-l mailing list
>>>>> BioSQL-l at open-bio.org
>>>>> http://open-bio.org/mailman/listinfo/biosql-l
>>>>>
>>>
>>>
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------